chr5-62777871-T-C

Variant names:

• chr5-62777871-T-C
• rs7715472

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.536 in 152,000 control chromosomes in the GnomAD database, including 22,030 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (22030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81413 AN: 151882 Hom.: 22000 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.517

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.536 AC: 81493 AN: 152000 Hom.: 22030 Cov.: 32 AF XY: 0.533 AC XY: 39633 AN XY: 74304

African (AFR) AF: 0.506 AC: 20944 AN: 41428

American (AMR) AF: 0.497 AC: 7598 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1945 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2321 AN: 5170

South Asian (SAS) AF: 0.595 AC: 2871 AN: 4822

European-Finnish (FIN) AF: 0.560 AC: 5908 AN: 10546

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38082 AN: 67968

Other (OTH) AF: 0.519 AC: 1095 AN: 2110

Alfa AF: 0.547 Hom.: 10949

Bravo AF: 0.526

Asia WGS AF: 0.534 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.1
DANN	Benign	0.85
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7715472; hg19: chr5-62073698;